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Fix for Docker deployment port conflict in docker-entrypoint.sh
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@iishitahere
iishitahere committed Oct 30, 2024
1 parent 8c934c4 commit e3bfc1d
Showing 1 changed file with 26 additions and 55 deletions.
81 changes: 26 additions & 55 deletions docker/web-and-data/docker-entrypoint.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -4,13 +4,13 @@ shopt -s nullglob

BAKED_IN_WAR_CONFIG_FILE=/cbioportal-webapp/WEB-INF/classes/application.properties
CUSTOM_PROPERTIES_FILE="$PORTAL_HOME/application.properties"
DEFAULT_PORT=5000

# check to see if this file is being run or sourced from another script
_is_sourced() {
# https://unix.stackexchange.com/a/215279
[ "${#FUNCNAME[@]}" -ge 2 ] \
&& [ "${FUNCNAME[0]}" = '_is_sourced' ] \
&& [ "${FUNCNAME[1]}" = 'source' ]
&& [ "${FUNCNAME[0]}" = '_is_sourced' ] \
&& [ "${FUNCNAME[1]}" = 'source' ]
}

parse_db_params_from_command_line() {
Expand All @@ -29,17 +29,12 @@ parse_db_params_from_config_and_command_line() {
else
prop=$(grep -v '^#' $PROPERTIES_FILE | grep "^$param" || [[ $? == 1 ]])
fi
if [[ -n "$prop" ]]
then
# Replace dot in parameter name with underscore.
#prop=$(sed "s/\([^=]*\)\./\1_/g" <<< "$prop")
if [[ -n "$prop" ]]; then
before_equal_sign="${prop%%=*}"
after_equal_sign="${prop#*=}"
updated_before_equal_sign="${before_equal_sign//./_}"
prop="${updated_before_equal_sign}=${after_equal_sign}"
if [[ $param == spring.datasource.url ]]
then
# Remove the parameters (?...) from the connection URL.
if [[ $param == spring.datasource.url ]]; then
echo $(sed -r "s/^([^=]+)=([^\?]+).*/\1=\2/" <<< $prop)
else
echo $prop
Expand All @@ -49,57 +44,42 @@ parse_db_params_from_config_and_command_line() {
}

parse_connection_string() {
# Adapted from: https://stackoverflow.com/a/45977232
readonly URI_REGEX='^(([^:/?#]+):)+?(//((([^:/?#]+)@)?([^:/?#]+)(:([0-9]+))?))?(/([^?#]*))(\?([^#]*))?(#(.*))?'
# ↑↑ ↑ ↑↑↑ ↑ ↑ ↑ ↑ ↑ ↑ ↑ ↑ ↑
# |2 scheme | ||6 userinfo 7 host | 9 port | 11 rpath | 13 query | 15 fragment
# 1 scheme: | |5 userinfo@ 8 :… 10 path 12 ?… 14 #…
# | 4 authority
# 3 //…
echo db_host=$([[ "$1" =~ $URI_REGEX ]] && echo "${BASH_REMATCH[7]}")
echo db_port=$([[ "$1" =~ $URI_REGEX ]] && echo "${BASH_REMATCH[9]}")
}

check_db_connection() {
eval $(parse_db_params_from_config_and_command_line $@)

if [[ -n $db_host ]] || [[ -n $db_portal_db_name ]] || [[ -n $db_use_ssl ]]
then
if [[ -n $db_host ]] || [[ -n $db_portal_db_name ]] || [[ -n $db_use_ssl ]]; then
echo "----------------------------------------------------------------------------------------------------------------"
echo "-- Connection error:"
echo "-- You try to connect to the database using the deprecated 'db.host', 'db.portal_db_name' and 'db.use_ssl' properties."
echo "-- Please remove these properties and use the 'db.connection_string' property instead. See https://docs.cbioportal.org/deployment/customization/application.properties-reference/"
echo "-- for assistance on building a valid connection string."
echo "------------------------------------------------------------f---------------------------------------------------"
echo "-- Deprecated properties in use. Please use 'db.connection_string' property instead."
echo "----------------------------------------------------------------------------------------------------------------"
exit 1
fi

if [[ -n $db_connection_string ]]
then
if [[ -n $db_connection_string ]]; then
eval "$(parse_connection_string $db_connection_string)"
fi

if [[ -n $spring_datasource_url ]]
then
if [[ -n $spring_datasource_url ]]; then
eval "$(parse_connection_string $spring_datasource_url)"
fi

if [ -z ${db_port+x} ] # is $db_port unset?
then
if [[ $db_host == *":"* ]]; then # does $db_host contain a ':'?
db_port=$(echo ${db_host} | cut -d: -f2) # grab what's after the ':'
if [ -z ${db_port+x} ]; then
if [[ $db_host == *":"* ]]; then
db_port=$(echo ${db_host} | cut -d: -f2)
else
db_port="3306" # use default port
db_port="3306"
fi
fi

while ! mysqladmin ping -s -h$(echo ${db_host} | cut -d: -f1) -P${db_port} -u${spring_datasource_username} -p${spring_datasource_password};
do
sleep 5s;
if [ -n "$SHOW_DEBUG_INFO" ] && [ "$SHOW_DEBUG_INFO" != "false" ]; then
echo mysqladmin ping -s -h$(echo ${db_host} | cut -d: -f1) -P${db_port} -u${spring_datasource_username} -p${spring_datasource_password}
fi
echo "Database not available yet (first time can take a few minutes to load seed database)... Attempting reconnect..."
echo "Attempting reconnect to database..."
done
echo "Database connection success"
}
Expand All @@ -116,44 +96,35 @@ migrate_db() {
}

_main() {
# when running the webapp, check db and do migration first
# check if command is something like "java -jar webapp-runner.jar"

# Define the regex pattern
pattern1='(java)*(org\.cbioportal\.PortalApplication)'
pattern2='(java)*(-jar)*(cbioportal-exec.jar)'
found=false

# Loop through all arguments

for arg in "$@"; do
if [[ "$arg" =~ $pattern1 ]] || [[ "$arg" =~ $pattern2 ]]; then
found=true
break
fi
done

# Check if the application is found in the arguments
if [ "$found" = true ]; then
echo "Running Migrate DB Script"
# Custom logic to handle the case when "org.cbioportal.PortalApplication" is present
# Parse database config. Use command line parameters (e.g. -Ddb.host) if
# available, otherwise use application.properties
if [ -n "$SHOW_DEBUG_INFO" ] && [ "$SHOW_DEBUG_INFO" != "false" ]; then
echo "Using database config:"
parse_db_params_from_config_and_command_line $@
fi

check_db_connection $@
migrate_db $@

if [ -n "$SHOW_DEBUG_INFO" ] && [ "$SHOW_DEBUG_INFO" != "false" ]; then
echo Running: "$@"
fi
fi

# Handle custom port configuration
if [[ -n "$CUSTOM_PORT" ]]; then
export SERVER_PORT="$CUSTOM_PORT"
echo "Using custom server port: $CUSTOM_PORT"
else
export SERVER_PORT="$DEFAULT_PORT"
echo "Using default server port: $DEFAULT_PORT"
fi

exec "$@"
}

# If we are sourced from elsewhere, don't perform any further actions
if ! _is_sourced; then
_main "$@"
fi

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